[Debian-med-packaging] Bug#948097: libbio-db-hts-perl: autopkgtest failure: Can't locate Bio/SeqFeature/Lite.pm in @INC

Paul Gevers elbrus at debian.org
Fri Jan 3 20:53:27 GMT 2020 

Source: libbio-db-hts-perl
Version: 3.01-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainers,

With a recent upload of libbio-db-hts-perl you added an autopkgtest to
libbio-db-hts-perl, great. However, it fails. I copied some of the
output at the bottom of this report.

Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=libbio-db-hts-perl

https://ci.debian.net/data/autopkgtest/testing/amd64/libb/libbio-db-hts-perl/3632505/log.gz

    1..22
    # Base class package "Bio::SeqFeature::Lite" is empty.
    #     (Perhaps you need to 'use' the module which defines that
package first,
    #     or make that module available in @INC (@INC contains:
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0
/usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30
/usr/share/perl/5.30 /usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base).
    #  at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457.
    not ok 1 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm line 457.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm line 457.
    not ok 2 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm exited
successfully
    ok 3 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Constants.pm exited
successfully
    ok 4 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Faidx.pm exited successfully
    ok 5 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/FetchIterator.pm exited
successfully
    ok 6 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq/Record.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm line 71.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm line 71.
    not ok 7 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm exited successfully
    ok 8 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Pileup.pm exited
successfully
    # Base class package "Bio::SeqFeature::Lite" is empty.
    #     (Perhaps you need to 'use' the module which defines that
package first,
    #     or make that module available in @INC (@INC contains:
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0
/usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30
/usr/share/perl/5.30 /usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base).
    #  at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm line 49.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm line 49.
    not ok 9 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    not ok 10 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm exited successfully
    ok 11 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/ReadIterator.pm exited
successfully
    # Name "Bio::DB::HTS::Segment::abs_ref" used only once: possible
typo at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70.
    # Name "Bio::DB::HTS::Segment::ref" used only once: possible typo at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70.
    # Name "Bio::DB::HTS::Segment::sourceseq" used only once: possible
typo at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70.
    ok 12 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm line 21.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm line 21.
    not ok 13 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm line 22.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm line 22.
    not ok 14 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm exited successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56.
    # Compilation failed in require at /usr/share/perl/5.30/base.pm line
137.
    # 	...propagated at /usr/share/perl/5.30/base.pm line 159.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Target.pm line 41.
    not ok 15 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Target.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3.
    not ok 16 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3.
    # Compilation failed in require at /usr/share/perl/5.30/base.pm line
137.
    # 	...propagated at /usr/share/perl/5.30/base.pm line 159.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/HeaderPtr.pm line 3.
    not ok 17 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/HeaderPtr.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm line 21.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm line 21.
    not ok 18 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5.
    not ok 19 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5.
    # Compilation failed in require at /usr/share/perl/5.30/base.pm line
137.
    # 	...propagated at /usr/share/perl/5.30/base.pm line 159.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/RowPtr.pm line 3.
    not ok 20 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/RowPtr.pm exited
successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # Compilation failed in require at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm line 408.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm line 408.
    not ok 21 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm exited successfully
    # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to
install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0
/usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    # BEGIN failed--compilation aborted at
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360.
    not ok 22 - /usr/bin/perl -wc
/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm exited successfully
not ok 4 - all modules in libbio-db-hts-perl pass the syntax check
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/4 subtests

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